Francis called on Mexico's government on Saturday to fight endemic corruption and drug trafficking and he then prayed with thousands before the icon that unites the country - the Virgin of Guadalupe.
Corruption is deeply ingrained in Mexico, and President Enrique Pena Nieto, his wife and finance minister have all been embroiled in conflict of interest scandals involving homes purchased from government contractors.
The pope also exhorted Mexico's bishops to take a more active stand against the drug trade, which he said "devours like a metastasis."
Drug-trafficking gangs have infiltrated police forces across the country and more than 100,000 people have been killed in drug violence over the last decade. Some 26,000 are missing.
"Experience teaches us that each time we seek the path of privilege or benefits for a few to the detriment of the good of all, sooner or later the life of society becomes a fertile soil for corruption, the drug trade, the exclusion of different cultures, violence and also human trafficking, kidnapping and death," the pope said in a speech to Pena Nieto, government ministers and foreign diplomats.
He said Mexico's leaders have a "particular duty" to move past corruption and violence and work for the collective good.
The pope later celebrated mass at the vast Basilica of our Lady Of Guadalupe. Some 5,000 mostly well-heeled spectators gathered inside the church, while at least five times as many spectators gathered outside under the beating sun.
Francis had said he yearned to visit the Basilica of Guadalupe, which attracts millions of pilgrims from all over Latin America, and to reflect silently in front of her image.
"'Don't be afraid,' that is what she tells me," the pope said ahead of his visit.
While inside a small niche behind the altar to venerate the icon, he lost his balance and fell back into a chair, causing the crowd to gasp, although it did not seem serious. After praying for about 20 minutes, the 79-year-old pope, who suffers from sciatica in one leg, stood up and walked out.
'BAD, CORRUPT, CRIMINALS'
Carrying pictures of the Virgin of Guadalupe, thousands converged on the basilica, many in family groups, some clutching coveted tickets to enter inside.
Guadalupe Nava, a 23-year-old lawyers, said the pope should ask the Virgin "to intercede for us, to put love in the hearts of those who are bad, the corrupt officials and the criminals."
In his three years as pope, Francis has repeatedly told political leaders as well as senior figures inside his own Church to do better, and earlier this month he urged Mexicans to fight against corruption and brutal drug gang violence.
Some Mexicans are looking to him to take that even further while he's here.
The country is still reeling from the abduction and apparent massacre of 43 trainee teachers by a drug gang in league with police in late 2014. The pope appeared to refer to them in his homily on Saturday, speaking of "children leaving, becoming lost or even being taken by criminals."
He has also taken a stand for migrants around the world, making it a central issue of his papacy, and he will end his visit to Mexico in the notorious northern border city of Ciudad Juarez, where he will meet relatives of victims of violence.
Speaking in his native Spanish before bishops inside Mexico City's main cathedral earlier on Saturday, the Argentine-born pontiff urged religious leaders to do more to help migrants, "pouring balm on their injured feet" through social and charity programs.
"Brothers, may your hearts be capable of following these men and women and reaching them beyond the borders," he said, calling on Mexico's Church to strengthen its ties to the U.S. episcopate.
From the U.S. border to the indigenous south, Francis will visit some of Mexico's poorest and most violent corners on his five-day trip.
He will say Mass with indigenous communities in Mexico's poorest state Chiapas, and speak with young people in Morelia, the capital of Michoacan state that has been plagued by violence between drug gangs and armed vigilante groups. In Juarez, he will also visit a prison.
In a reminder of Mexico's corruption and violence, 49 people were killed in a fight between rival gangs in a prison just days before the pope's arrival.
